XGR (version 1.1.4)

xGRoverlap: Function to extract overlap-based scores given a list of genomic regions

Description

xGRoverlap is supposed to extract overlap-based scores given a list of genomic regions. Scores are extracted for overlapped sub-regions only, valued at the mean per base; otherwise NA. It returns a GR object.

Usage

xGRoverlap(data, format = c("chr:start-end", "data.frame", "bed",
"GRanges"),
build.conversion = c(NA, "hg38.to.hg19", "hg18.to.hg19"), GR.score =
c(NA,
"RecombinationRate", "phastCons100way", "phyloP100way", "GERP"),
verbose = T, RData.location = "http://galahad.well.ox.ac.uk/bigdata")

Arguments

data

input genomic regions (GR). If formatted as "chr:start-end" (see the next parameter 'format' below), GR should be provided as a vector in the format of 'chrN:start-end', where N is either 1-22 or X, start (or end) is genomic positional number; for example, 'chr1:13-20'. If formatted as a 'data.frame', the first three columns correspond to the chromosome (1st column), the starting chromosome position (2nd column), and the ending chromosome position (3rd column). If the format is indicated as 'bed' (browser extensible data), the same as 'data.frame' format but the position is 0-based offset from chromomose position. If the genomic regions provided are not ranged but only the single position, the ending chromosome position (3rd column) is allowed not to be provided. The data could also be an object of 'GRanges' (in this case, formatted as 'GRanges')

format

the format of the input data. It can be one of "data.frame", "chr:start-end", "bed" or "GRanges"

build.conversion

the conversion from one genome build to another. The conversions supported are "hg38.to.hg19" and "hg18.to.hg19". By default it is NA (no need to do so)

GR.score

the genomic regions together with score data. By default, it is 'NA' to disable this option. Pre-built genomic score data: 'RecombinationRate' (recombintion rate, http://www.ncbi.nlm.nih.gov/pubmed/17943122)), 'phastCons100way', 'phyloP100way', 'GERP'. Beyond pre-built data, the user can specify the customised input: load your customised GR object directly (with the first meta column for scores; if not provided, it will be valued at 1)

verbose

logical to indicate whether the messages will be displayed in the screen. By default, it sets to true for display

RData.location

the characters to tell the location of built-in RData files. See xRDataLoader for details

Value

a GenomicRanges object, appended with a meta-column 'GScore'. If input data contains only a genomic region, then outputs are all overlapped regions from GR.score; otherwise all overlapped regions from input data will be output.

See Also

xRDataLoader

Examples

# NOT RUN {
# Load the XGR package and specify the location of built-in data
library(XGR)
RData.location <- "http://galahad.well.ox.ac.uk/bigdata"

# a) provide the genomic regions
## load ImmunoBase
ImmunoBase <- xRDataLoader(RData.customised='ImmunoBase',
RData.location=RData.location)
## get lead SNPs reported in AS GWAS
data <- ImmunoBase$AS$variant

# b) extract recombination rate
gr <- xGRoverlap(data=data, format="GRanges",
GR.score="RecombinationRate", RData.location=RData.location)

############################################
# gene-centric genomic score (per base)
gr_Gene <- xRDataLoader('UCSC_knownGene',
RData.location=RData.location)
## recombination rate
gr_rr <- xGRoverlap(data=gr_Gene, format="GRanges",
GR.score="RecombinationRate", RData.location=RData.location)
## phastCons100way
gr_phast <- xGRoverlap(data=gr_Gene, format="GRanges",
GR.score="phastCons100way", RData.location=RData.location)
## phyloP100way
gr_phylo <- xGRoverlap(data=gr_Gene, format="GRanges",
GR.score="phyloP100way", RData.location=RData.location)
# }